+Open data
-Basic information
Entry | Database: PDB / ID: 1qbj | ||||||
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Title | CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX | ||||||
Components |
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Keywords | HYDROLASE/DNA / PROTEIN-Z-DNA COMPLEX / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing ...somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / hematopoietic stem cell homeostasis / response to interferon-alpha / adenosine to inosine editing / RISC complex assembly / pre-miRNA processing / negative regulation of hepatocyte apoptotic process / definitive hemopoiesis / negative regulation of type I interferon-mediated signaling pathway / hepatocyte apoptotic process / positive regulation of viral genome replication / RNA processing / hematopoietic progenitor cell differentiation / protein export from nucleus / erythrocyte differentiation / response to virus / PKR-mediated signaling / mRNA processing / cellular response to virus / osteoblast differentiation / protein import into nucleus / double-stranded RNA binding / Interferon alpha/beta signaling / defense response to virus / innate immune response / nucleolus / DNA binding / RNA binding / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2.1 Å | ||||||
Authors | Schwartz, T. / Rould, M.A. / Rich, A. | ||||||
Citation | Journal: Science / Year: 1999 Title: Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Authors: Schwartz, T. / Rould, M.A. / Lowenhaupt, K. / Herbert, A. / Rich, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qbj.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qbj.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/1qbj ftp://data.pdbj.org/pub/pdb/validation_reports/qb/1qbj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: DNA chain | Mass: 2114.398 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: SYNTHETIC #2: Protein | Mass: 9002.293 Da / Num. of mol.: 3 / Fragment: N-TERMINAL HELIX-TURN-HELIX DOMAIN ZALPHA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): NOVABLUE (DE3) / References: UniProt: P55265 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37 % | |||||||||||||||
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Crystal grow | pH: 5.6 Details: HANGING DROP VAPOR DIFFUSION OVER 1.6 M (NH4)2SO4, 10 % GLYCEROL AT 24 DEGREES CELSIUS, pH 5.6 | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 29702 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rsym value: 0.074 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.535 / % possible all: 99.3 |
Reflection | *PLUS Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.535 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.1→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 29.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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